I took a fresh triplet of photos just now and made an HDR photo and then Cropped, and it worked: no problem.
So I haven't been able to reproduce it with other files, just the first one I tried. (and it still does it)
Since I'm not imagining this, I speculate: The first one was hand-held while the one I tried just now was braced against a post. Perhaps it relates to the internal cropping caused by auto-alignment?
Also, the one I did just now was a Portrait Orientation. The problem one was Landscape. (I'm stretching here...)
I'd suggest you post over on the feedback forum (if you haven't, already) and include a link to the HDR that's acting strangely. Upload it to www.dropbox.com and post a public download link, there/here.